Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013283.1 Corchorus olitorius cultivar O-4 contig13316, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 59667
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:4342 original size:17 final size:18
Alignment explanation
Indices: 4320--4355 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
4310 CAAGGGTAAT
*
4320 TAAAAA-AATTGTTTTCA
1 TAAAAAGAAGTGTTTTCA
4337 TAAAAAGAAGTGTTTTCA
1 TAAAAAGAAGTGTTTTCA
4355 T
1 T
4356 GATAGAGGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (18 bp):
TAAAAAGAAGTGTTTTCA
Found at i:4894 original size:16 final size:15
Alignment explanation
Indices: 4873--4902 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
4863 GTATGAATTC
4873 AAATTGATTTCTTGAA
1 AAATTGATTT-TTGAA
4889 AAATTGATTTTTGA
1 AAATTGATTTTTGA
4903 TTAACTTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.37, C:0.03, G:0.13, T:0.47
Consensus pattern (15 bp):
AAATTGATTTTTGAA
Found at i:7596 original size:24 final size:25
Alignment explanation
Indices: 7569--7623 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
7559 ATTAAAAACA
*
7569 AAAAATAAGAACTTTTTTT-AACGC
1 AAAAAGAAGAACTTTTTTTAAACGC
**
7593 AAAAAGAAGATTTTTTTTTAAAACGC
1 AAAAAGAAGAACTTTTTTT-AAACGC
7619 AAAAA
1 AAAAA
7624 AATAAAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 16 0.62
26 10 0.38
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.31
Consensus pattern (25 bp):
AAAAAGAAGAACTTTTTTTAAACGC
Found at i:9262 original size:18 final size:19
Alignment explanation
Indices: 9239--9278 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
9229 TTCTTGAAAT
9239 AATTCTTC-AATGATCTTC
1 AATTCTTCAAATGATCTTC
*
9257 AATTCTTCAAATTATCTTC
1 AATTCTTCAAATGATCTTC
9276 AAT
1 AAT
9279 CAAGAACTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.33, C:0.20, G:0.03, T:0.45
Consensus pattern (19 bp):
AATTCTTCAAATGATCTTC
Found at i:9932 original size:64 final size:64
Alignment explanation
Indices: 9831--9964 Score: 214
Period size: 64 Copynumber: 2.1 Consensus size: 64
9821 TGAATTTCGG
* *
9831 TTGATCTAGGGTGATCTCTCTACAATGAATTTCAATTGGCTCAGGATGGTCGATCTTAAGTTAA
1 TTGATCTAGGGTGATCTCTCTACAATGAATTTCAATTGGCCCAGGATGGTCCATCTTAAGTTAA
* * * *
9895 TTGATCTAGGGTTATCTCTCTATAGTGAATTTCAATTGGCCCAGGGTGGTCCATCTTAAGTTAA
1 TTGATCTAGGGTGATCTCTCTACAATGAATTTCAATTGGCCCAGGATGGTCCATCTTAAGTTAA
9959 TTGATC
1 TTGATC
9965 CAAGGGTCTC
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (64 bp):
TTGATCTAGGGTGATCTCTCTACAATGAATTTCAATTGGCCCAGGATGGTCCATCTTAAGTTAA
Found at i:10014 original size:95 final size:96
Alignment explanation
Indices: 9895--10171 Score: 362
Period size: 95 Copynumber: 2.9 Consensus size: 96
9885 CTTAAGTTAA
9895 TTGATCTAGGGTTATCTCTCTATAGTGAATTTCAATTGGCCCAGGGTGGTCCATCTTAAGTTAAT
1 TTGATCTAGGGTTATCTCTCTATAGTGAATTTCAATTGGCCCAGGGTGGTCCATCTTAAGTTAAT
*
9960 TGATCCAAGGG-TCTCTCTAGTGAATTTTGG
66 TGATCCAAGGGATCTCTCTAGTGAATTTCGG
* * *
9990 TTGATCCATGGTTATCTCTCTATAGTGAATTTCAATTGGCCCATGGTGGTCCATCTTAAGTTAAT
1 TTGATCTAGGGTTATCTCTCTATAGTGAATTTCAATTGGCCCAGGGTGGTCCATCTTAAGTTAAT
* *
10055 TGATCGAGGGTGATCTTTCTCTAGTGAATTTCGG
66 TGATCCAAGG-GATC--TCTCTAGTGAATTTCGG
* * ** * * *
10089 TTGATCTAGGGTGATCTCT-TCACAGTGTGTTTCAAGTGACCCAGGGCGGTCCATCTTAAGTTAA
1 TTGATCTAGGGTTATCTCTCT-ATAGTGAATTTCAATTGGCCCAGGGTGGTCCATCTTAAGTTAA
* *
10153 TTGGTCC-AGGGCTCTCTCT
65 TTGATCCAAGGGATCTCTCT
10172 TTAGCAAATT
Statistics
Matches: 157, Mismatches: 20, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
95 75 0.48
96 1 0.01
97 5 0.03
98 3 0.02
99 73 0.46
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (96 bp):
TTGATCTAGGGTTATCTCTCTATAGTGAATTTCAATTGGCCCAGGGTGGTCCATCTTAAGTTAAT
TGATCCAAGGGATCTCTCTAGTGAATTTCGG
Found at i:10040 original size:159 final size:161
Alignment explanation
Indices: 9771--10086 Score: 451
Period size: 159 Copynumber: 2.0 Consensus size: 161
9761 GGTTTACTGA
*
9771 CCCAGGGTGGTCCATCTTCAGTTAATTGATCCAGGGAAATCTCTCTTCAGTGAATTTCGGTTGAT
1 CCCAGGGTGGTCCATCTTAAGTTAATTGATCCAGGG--ATCTCTCTTCAGTGAATTTCGGTTGAT
* * *
9836 CTAGGGTGATCTCTCTACAATGAATTTCAATTGGCTCAGGATGGTCGATCTTAAGTTAATTGATC
64 CCAGGGTGATCTCTCTACAATGAATTTCAATTGGCCCAGGATGGTCCATCTTAAGTTAATTGATC
* *
9901 TAGGGTTATCTCTCTATAGTGAATTTCAATTGG
129 GAGGGTGATCTCTCTATAGTGAATTTCAATTGG
*
9934 CCCAGGGTGGTCCATCTTAAGTTAATTGATCCAAGGG-TCTCTC-T-AGTGAATTTTGGTTGATC
1 CCCAGGGTGGTCCATCTTAAGTTAATTGATCC-AGGGATCTCTCTTCAGTGAATTTCGGTTGATC
* * * *
9996 CATGGTTATCTCTCTATAGTGAATTTCAATTGGCCCATGG-TGGTCCATCTTAAGTTAATTGATC
65 CAGGGTGATCTCTCTACAATGAATTTCAATTGGCCCA-GGATGGTCCATCTTAAGTTAATTGATC
* *
10060 GAGGGTGATCTTTCTCTAGTGAATTTC
129 GAGGGTGATCTCTCTATAGTGAATTTC
10087 GGTTGATCTA
Statistics
Matches: 138, Mismatches: 13, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
159 94 0.68
160 3 0.02
161 6 0.04
163 31 0.22
164 4 0.03
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (161 bp):
CCCAGGGTGGTCCATCTTAAGTTAATTGATCCAGGGATCTCTCTTCAGTGAATTTCGGTTGATCC
AGGGTGATCTCTCTACAATGAATTTCAATTGGCCCAGGATGGTCCATCTTAAGTTAATTGATCGA
GGGTGATCTCTCTATAGTGAATTTCAATTGG
Found at i:10206 original size:99 final size:97
Alignment explanation
Indices: 9895--10223 Score: 325
Period size: 99 Copynumber: 3.4 Consensus size: 97
9885 CTTAAGTTAA
* * *
9895 TTGATCTAGGGTTATCTCTC-T-ATAGTGAATTTCAATTGGCCCAGGGTGGTCCATCTTAAGTTA
1 TTGATCCAGGGTGATCTCTCTTCACAGTGAATTTCAATTGGCCCAGGGTGGTCCATCTTAAGTTA
*
9958 ATTGATCCAAGGGTCTCTC-TAGTGAATTTTGG
66 ATTGATCC-AGGGTCTCTCTTAGTGAATTTCGG
* * * *
9990 TTGATCCATGGTTATCTCTC-T-ATAGTGAATTTCAATTGGCCCATGGTGGTCCATCTTAAGTTA
1 TTGATCCAGGGTGATCTCTCTTCACAGTGAATTTCAATTGGCCCAGGGTGGTCCATCTTAAGTTA
* *
10053 ATTGATCGAGGGTGATCTTTCTCTAGTGAATTTCGG
66 ATTGATCCA-GG-G-TCTCTCT-TAGTGAATTTCGG
* ** * * *
10089 TTGATCTAGGGTGA--TCTCTTCACAGTGTGTTTCAAGTGACCCAGGGCGGTCCATCTTAAGTTA
1 TTGATCCAGGGTGATCTCTCTTCACAGTGAATTTCAATTGGCCCAGGGTGGTCCATCTTAAGTTA
* ** **
10152 ATTGGTCCAGGGCTCTCTCTTTAGCAAATTTCAA
66 ATTGATCCAGGG-TCTCTC-TTAGTGAATTTCGG
* *
10186 TTGATCCAGGGCGATCTCTCTT--CAGTAAATTTCAATTG
1 TTGATCCAGGGTGATCTCTCTTCACAGTGAATTTCAATTG
10224 ATCTAGGGCG
Statistics
Matches: 194, Mismatches: 30, Indels: 18
0.80 0.12 0.07
Matches are distributed among these distances:
94 1 0.01
95 69 0.36
96 1 0.01
97 48 0.25
98 4 0.02
99 71 0.37
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (97 bp):
TTGATCCAGGGTGATCTCTCTTCACAGTGAATTTCAATTGGCCCAGGGTGGTCCATCTTAAGTTA
ATTGATCCAGGGTCTCTCTTAGTGAATTTCGG
Found at i:10266 original size:34 final size:35
Alignment explanation
Indices: 10151--10278 Score: 147
Period size: 35 Copynumber: 3.7 Consensus size: 35
10141 ATCTTAAGTT
* * *
10151 AATTGGTCCAGGGC--TCTCTCTTTAGCAAATTTC
1 AATTGATCCAGGGCGATCTCTCTTCAGTAAATTTC
10184 AATTGATCCAGGGCGATCTCTCTTCAGTAAATTTC
1 AATTGATCCAGGGCGATCTCTCTTCAGTAAATTTC
* *
10219 AATTGATCTAGGGCGGTCTCTCTTC-G-ATAATTTC
1 AATTGATCCAGGGCGATCTCTCTTCAGTA-AATTTC
* * *
10253 GATTAATCCAGGGCGATCTTTCTTCA
1 AATTGATCCAGGGCGATCTCTCTTCA
10279 TTTCCATTGA
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
33 14 0.17
34 27 0.33
35 40 0.49
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.36
Consensus pattern (35 bp):
AATTGATCCAGGGCGATCTCTCTTCAGTAAATTTC
Found at i:10333 original size:51 final size:51
Alignment explanation
Indices: 10278--10379 Score: 143
Period size: 51 Copynumber: 2.0 Consensus size: 51
10268 ATCTTTCTTC
* *
10278 ATTTC-CATTGACGGAGGGTGGTCTTTCTTTAATTCTTCAATACTTCAATTT
1 ATTTCACAATGACGG-GGGTGGTCTTTCTTCAATTCTTCAATACTTCAATTT
* * *
10329 ATTTCAGAATGATGGGGGTGGTCTTTCTTCAATTCTTCAATGCTTCAATTT
1 ATTTCACAATGACGGGGGTGGTCTTTCTTCAATTCTTCAATACTTCAATTT
10380 GAATTCTTCA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
51 39 0.87
52 6 0.13
ACGTcount: A:0.22, C:0.17, G:0.18, T:0.44
Consensus pattern (51 bp):
ATTTCACAATGACGGGGGTGGTCTTTCTTCAATTCTTCAATACTTCAATTT
Found at i:10366 original size:8 final size:8
Alignment explanation
Indices: 10353--10789 Score: 217
Period size: 8 Copynumber: 54.1 Consensus size: 8
10343 GGGGTGGTCT
10353 TTCTTCAA
1 TTCTTCAA
10361 TTCTTCAA
1 TTCTTCAA
*
10369 TGCTTCAA
1 TTCTTCAA
*
10377 -T-TTGAA
1 TTCTTCAA
10383 TTCTTCAA
1 TTCTTCAA
*
10391 TTATTCAA
1 TTCTTCAA
10399 -T-TTCAA
1 TTCTTCAA
10405 TTCATT-AA
1 TTC-TTCAA
*
10413 TACTTCAA
1 TTCTTCAA
*
10421 TGCTTCAA
1 TTCTTCAA
10429 -T-TTCAA
1 TTCTTCAA
* *
10435 ATCTTGAA
1 TTCTTCAA
*
10443 TTATTCAA
1 TTCTTCAA
10451 TTCTTCAA
1 TTCTTCAA
*
10459 TTATTCAA
1 TTCTTCAA
* *
10467 TGCTTCAC
1 TTCTTCAA
10475 TTCTTCAA
1 TTCTTCAA
*
10483 TGCTTCAA
1 TTCTTCAA
*
10491 TTTATTCTAA
1 -TTCTTC-AA
* ** *
10501 GGATGATCAGGG
1 --TTCTTCA--A
** *
10513 TTGGTC-T
1 TTCTTCAA
10520 TTCTTCAA
1 TTCTTCAA
*
10528 TTCTTCGA
1 TTCTTCAA
*
10536 TTATTCAA
1 TTCTTCAA
* *
10544 TGCTTTAA
1 TTCTTCAA
*
10552 CTCTTCAA
1 TTCTTCAA
* *
10560 TTATTTAA
1 TTCTTCAA
* *
10568 TGCTTCGA
1 TTCTTCAA
*
10576 TTGTTCAA
1 TTCTTCAA
*
10584 TTATTCAA
1 TTCTTCAA
*
10592 TGCTTCAA
1 TTCTTCAA
10600 TTCTTCAA
1 TTCTTCAA
*
10608 TTATTCAA
1 TTCTTCAA
**
10616 AGCTTCAA
1 TTCTTCAA
*
10624 TTTTTCAA
1 TTCTTCAA
*
10632 TTATTCAA
1 TTCTTCAA
*
10640 TGCTTCAAA
1 TTCTTC-AA
10649 TTCTTCAA
1 TTCTTCAA
* *
10657 TTATTTAA
1 TTCTTCAA
*
10665 TGCTTCAAA
1 TTCTTC-AA
10674 TTCTTCAA
1 TTCTTCAA
*
10682 TTATTCAA
1 TTCTTCAA
*
10690 TGCTTCAA
1 TTCTTCAA
10698 TTCTTCAA
1 TTCTTCAA
*
10706 TTATTCAA
1 TTCTTCAA
* *
10714 TGCTGCAA
1 TTCTTCAA
10722 TTCTTCAA
1 TTCTTCAA
* *
10730 TGCTTAAAA
1 TTCTT-CAA
10739 TT-TTCAA
1 TTCTTCAA
*
10746 TTATTCAA
1 TTCTTCAA
* *
10754 TGCATTTTTAA
1 T---TCTTCAA
*
10765 TTCTTCCA
1 TTCTTCAA
*
10773 TGCTTCAA
1 TTCTTCAA
10781 TTCTTCAA
1 TTCTTCAA
10789 T
1 T
10790 GCTTTAATTT
Statistics
Matches: 313, Mismatches: 95, Indels: 42
0.70 0.21 0.09
Matches are distributed among these distances:
6 14 0.04
7 14 0.04
8 246 0.79
9 23 0.07
10 7 0.02
11 9 0.03
ACGTcount: A:0.29, C:0.19, G:0.07, T:0.46
Consensus pattern (8 bp):
TTCTTCAA
Found at i:10387 original size:22 final size:22
Alignment explanation
Indices: 10356--10493 Score: 99
Period size: 22 Copynumber: 6.1 Consensus size: 22
10346 GTGGTCTTTC
*
10356 TTCAATTCTTCAATGCTTCAAT
1 TTCAATTCTTCAATACTTCAAT
*
10378 TTGAATTCTTCAATTA-TTCAAT
1 TTCAATTCTTCAA-TACTTCAAT
10400 TTCAATTCATT-AATACTTCAAT
1 TTCAATTC-TTCAATACTTCAAT
*
10422 GCTTCAA-T-TTCAA-ATCTTGAATT
1 --TTCAATTCTTCAATA-CTTCAA-T
10445 ATTCAATTCTTCAATTA-TTCAAT
1 -TTCAATTCTTCAA-TACTTCAAT
* *
10468 GCTTCACTTCTTCAATGCTTCAAT
1 --TTCAATTCTTCAATACTTCAAT
10492 TT
1 TT
10494 ATTCTAAGGA
Statistics
Matches: 93, Mismatches: 9, Indels: 28
0.72 0.07 0.22
Matches are distributed among these distances:
21 5 0.05
22 47 0.51
23 8 0.09
24 32 0.34
26 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.04, T:0.46
Consensus pattern (22 bp):
TTCAATTCTTCAATACTTCAAT
Found at i:10473 original size:24 final size:24
Alignment explanation
Indices: 10355--10730 Score: 320
Period size: 24 Copynumber: 15.6 Consensus size: 24
10345 GGTGGTCTTT
**
10355 CTTCAATTCTTCAATGCTTCAAT-
1 CTTCAATTCTTCAATTATTCAATG
*
10378 -TTGAATTCTTCAATTATTCAAT-
1 CTTCAATTCTTCAATTATTCAATG
10400 -TTCAATTCATT-AA-TACTTCAATG
1 CTTCAATTC-TTCAATTA-TTCAATG
* * * *
10423 CTTCAA-T-TTCAAATCTTGAATT
1 CTTCAATTCTTCAATTATTCAATG
*
10445 ATTCAATTCTTCAATTATTCAATG
1 CTTCAATTCTTCAATTATTCAATG
* ** *
10469 CTTCACTTCTTCAATGCTTCAATTT
1 CTTCAATTCTTCAATTATTCAA-TG
* * ** * ** * *
10494 ATTCTAAGGATGATCAGGGTTGGTC-TTT
1 CTTC-AA--TTCTTCA--ATTATTCAATG
*
10522 CTTCAATTCTTCGATTATTCAATG
1 CTTCAATTCTTCAATTATTCAATG
* * *
10546 CTTTAACTCTTCAATTATTTAATG
1 CTTCAATTCTTCAATTATTCAATG
* *
10570 CTTCGATTGTTCAATTATTCAATG
1 CTTCAATTCTTCAATTATTCAATG
*
10594 CTTCAATTCTTCAATTATTCAAAG
1 CTTCAATTCTTCAATTATTCAATG
*
10618 CTTCAATTTTTCAATTATTCAATG
1 CTTCAATTCTTCAATTATTCAATG
*
10642 CTTCAAATTCTTCAATTATTTAATG
1 CTTC-AATTCTTCAATTATTCAATG
10667 CTTCAAATTCTTCAATTATTCAATG
1 CTTC-AATTCTTCAATTATTCAATG
10692 CTTCAATTCTTCAATTATTCAATG
1 CTTCAATTCTTCAATTATTCAATG
*
10716 CTGCAATTCTTCAAT
1 CTTCAATTCTTCAAT
10731 GCTTAAAATT
Statistics
Matches: 282, Mismatches: 55, Indels: 31
0.77 0.15 0.08
Matches are distributed among these distances:
21 4 0.01
22 46 0.16
23 9 0.03
24 155 0.55
25 53 0.19
26 1 0.00
27 2 0.01
28 9 0.03
30 3 0.01
ACGTcount: A:0.29, C:0.19, G:0.07, T:0.45
Consensus pattern (24 bp):
CTTCAATTCTTCAATTATTCAATG
Found at i:10775 original size:19 final size:19
Alignment explanation
Indices: 10738--10791 Score: 51
Period size: 19 Copynumber: 3.0 Consensus size: 19
10728 AATGCTTAAA
10738 ATTTTCAATTATTCAATGC
1 ATTTTCAATTATTCAATGC
* * *
10757 ATTTTTAATTCTTCCATGC
1 ATTTTCAATTATTCAATGC
*
10776 ---TTCAATTCTTCAATGC
1 ATTTTCAATTATTCAATGC
10792 TTTAATTTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
16 14 0.47
19 16 0.53
ACGTcount: A:0.26, C:0.20, G:0.06, T:0.48
Consensus pattern (19 bp):
ATTTTCAATTATTCAATGC
Found at i:11002 original size:68 final size:67
Alignment explanation
Indices: 10925--11059 Score: 155
Period size: 68 Copynumber: 2.0 Consensus size: 67
10915 TTGGGGGTCT
* * * ***
10925 TTCTCCAATTCTTCAATTA-TTTAATGCTTCAATTTATTTCAGAATGATTGGGGGTGGTCTTTCA
1 TTCTCCAATTATCCAA-TACTTCAATGCTTCAATTTATTTCAG-ATGATCCAGGGTGGTCTTTCA
10989 TCAA
64 TCAA
* * * *
10993 TTCTTCAATTATCCAATACTTCAATTCTTCAATTTATTTTAGTTGATCCAGGGTGGTCTTTCATC
1 TTCTCCAATTATCCAATACTTCAATGCTTCAATTTATTTCAGATGATCCAGGGTGGTCTTTCATC
11058 AA
66 AA
11060 CTTATGTCGG
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
67 23 0.41
68 33 0.59
ACGTcount: A:0.25, C:0.18, G:0.13, T:0.44
Consensus pattern (67 bp):
TTCTCCAATTATCCAATACTTCAATGCTTCAATTTATTTCAGATGATCCAGGGTGGTCTTTCATC
AA
Found at i:11239 original size:31 final size:32
Alignment explanation
Indices: 11201--11297 Score: 133
Period size: 32 Copynumber: 3.1 Consensus size: 32
11191 CTTTTGCACA
11201 CCACTATATGGGGGCGTTTTATGAA-AAAACG
1 CCACTATATGGGGGCGTTTTATGAACAAAACG
** * *
11232 CCACTATACAGAGGCGTTTTATGAATAAAACG
1 CCACTATATGGGGGCGTTTTATGAACAAAACG
* *
11264 CCACTATATGGGTGTGTTTTATGAACAAAACG
1 CCACTATATGGGGGCGTTTTATGAACAAAACG
11296 CC
1 CC
11298 CATAAACGCC
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
31 22 0.39
32 34 0.61
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.27
Consensus pattern (32 bp):
CCACTATATGGGGGCGTTTTATGAACAAAACG
Found at i:13188 original size:7 final size:7
Alignment explanation
Indices: 13178--13210 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
13168 CTATATTGGG
13178 TTTTTAT
1 TTTTTAT
13185 TTTTTAT
1 TTTTTAT
13192 TTTTTAT
1 TTTTTAT
*
13199 TTATT-T
1 TTTTTAT
13205 TTTTTA
1 TTTTTA
13211 AGGAAAGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTTAT
Found at i:19749 original size:46 final size:46
Alignment explanation
Indices: 19682--19836 Score: 283
Period size: 46 Copynumber: 3.4 Consensus size: 46
19672 TGAGTAATTA
* *
19682 TCACACTGGATCAAGAGGTAATTAGTTAAAGAATAAAAGGGATACT
1 TCACACTGGATCAAGAGGTAATTATTTAAAGAATAAAAGGGATAAT
19728 TCACACTGGATCAAGAGGTAATTATTTAAAGAATAAAAGGGATAAT
1 TCACACTGGATCAAGAGGTAATTATTTAAAGAATAAAAGGGATAAT
*
19774 TCACACTGGATCAAGAGGTAATTATTTAAAGAATAAAAAGGATAAT
1 TCACACTGGATCAAGAGGTAATTATTTAAAGAATAAAAGGGATAAT
19820 TCACACTGGATCAAGAG
1 TCACACTGGATCAAGAG
19837 TTTTATCTAA
Statistics
Matches: 106, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 106 1.00
ACGTcount: A:0.45, C:0.11, G:0.20, T:0.25
Consensus pattern (46 bp):
TCACACTGGATCAAGAGGTAATTATTTAAAGAATAAAAGGGATAAT
Found at i:44024 original size:77 final size:74
Alignment explanation
Indices: 43925--44078 Score: 238
Period size: 77 Copynumber: 2.0 Consensus size: 74
43915 TAAATGAATC
* *
43925 TGAACTATAAGAAATGTAGAAATGCCAAAGGTGCCTATCAAGATTTTTTTTGGTTTTTCTTCAAA
1 TGAACTATAAGAAATGCAGAAATGCCAAAGGTGCCTATCAAGA-TTTTTTTGG-GTTT-TTCAAA
43990 ATGCAATTTAGA
63 ATGCAATTTAGA
*
44002 TGAACTATGAA-AAATGCGGAAATGCCAAAGGTGCCTATCAAGATTTTTTTGGGTTTTTCAAAAT
1 TGAACTAT-AAGAAATGCAGAAATGCCAAAGGTGCCTATCAAGATTTTTTTGGGTTTTTCAAAAT
44066 GCAATTTAGA
65 GCAATTTAGA
44076 TGA
1 TGA
44079 CCAGATATGA
Statistics
Matches: 73, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
74 21 0.29
75 3 0.04
76 9 0.12
77 38 0.52
78 2 0.03
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.34
Consensus pattern (74 bp):
TGAACTATAAGAAATGCAGAAATGCCAAAGGTGCCTATCAAGATTTTTTTGGGTTTTTCAAAATG
CAATTTAGA
Found at i:44160 original size:27 final size:27
Alignment explanation
Indices: 44122--44174 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
44112 AGCTTAAAAT
44122 GACTAAAATGCCCCTGAACATGCAAAG
1 GACTAAAATGCCCCTGAACATGCAAAG
*
44149 GACTAAAATGCCCTTGAACATGCAAA
1 GACTAAAATGCCCCTGAACATGCAAA
44175 AGTCCCAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.42, C:0.25, G:0.17, T:0.17
Consensus pattern (27 bp):
GACTAAAATGCCCCTGAACATGCAAAG
Found at i:44185 original size:28 final size:27
Alignment explanation
Indices: 44126--44190 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
44116 TAAAATGACT
*
44126 AAAATGCCCCTGAACATGCAAAGGACT
1 AAAATGCCCCTGAACATGCAAAGGACC
* **
44153 AAAATGCCCTTGAACATGCAAAAGTCCC
1 AAAATGCCCCTGAACATGC-AAAGGACC
44181 AAAATGCCCC
1 AAAATGCCCC
44191 AAAATGACCC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 18 0.56
28 14 0.44
ACGTcount: A:0.40, C:0.29, G:0.15, T:0.15
Consensus pattern (27 bp):
AAAATGCCCCTGAACATGCAAAGGACC
Found at i:44761 original size:30 final size:30
Alignment explanation
Indices: 44707--45614 Score: 906
Period size: 30 Copynumber: 30.2 Consensus size: 30
44697 TTAACTGATG
* *
44707 AAGCAATGATCCTAAACCGGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* * * *
44737 AAGCAACGATCGTCAACCATGATTAAAACA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
** *
44767 AAGCAACAATCCT-AAGCCAGGATTAAAACA
1 AAGCAATGATCCTCAA-CCAGGATTAAAATA
** *
44797 AAGCAACAATCCTAAACCAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* * *
44827 AAGTAAAGATCCTCAACCAGGATTAAAATG
1 AAGCAATGATCCTCAACCAGGATTAAAATA
*
44857 GAGCAATGATCCTCAACCAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
*
44887 AAGCAATGATCCTAAACCAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* *
44917 AAACAATGATCCTCAAACAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* * * * ** * *
44947 AAGCAATGATAAAGCAATGATCCTCAACCAGGATTAAAACA
1 AAGCAATGAT----C-CTCA-AC-C-A--GGATTAAAA-TA
** * *
44988 AAGCAACAATCCTAAACCAGGATTAAAACA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
** *
45018 AAGCAACAATCCTAAACCAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* * *
45048 AAGTAAAGATCCTCAACCAGGATTAAAATG
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* *
45078 GAGCAATGATCCTCAACCAAGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* *
45108 AAGCAATGATCCTAAACCAGGATTAAAACA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
** * **
45138 AAGCAACAATCCTAAACCAGGATTAAAGCA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
*
45168 AAGCAATGATCCTAAACCAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* *
45198 AAGCAATGATCTTCAAACAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
** * *
45228 AAGCAATGATTTTCAAACATGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* *
45258 AAGCAATGATCCTAAACCAGGATTAAAACA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
** * * *
45288 AAGCAACAATCATAAATCAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* * *
45318 AAGTAAAGTTCCTCAACCAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* * * *
45348 AAGTAAAGTTCCTCAACCAGGATTAAAATG
1 AAGCAATGATCCTCAACCAGGATTAAAATA
*
45378 GAGCAATGATCCTCAACCAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
*
45408 AAGCAATGATCCTAAACCAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
*
45438 AAGCAACGATCCTCAACCAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* * * *
45468 AAGTAACGATCCTCAACTAGGATTAAAATG
1 AAGCAATGATCCTCAACCAGGATTAAAATA
*
45498 ATGCAAAT-ATCCTCAACCAGGATTAAAAT-
1 AAGC-AATGATCCTCAACCAGGATTAAAATA
45527 AA-C---GATCCTCAACCAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
*
45553 AAGTAAAT-ATCCTCAACCAGGATTAAAAT-
1 AAG-CAATGATCCTCAACCAGGATTAAAATA
*
45582 --G--ACGATCCTCAACCAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
45608 AAGCAAT
1 AAGCAAT
45615 TAAAGCAATA
Statistics
Matches: 742, Mismatches: 109, Indels: 54
0.82 0.12 0.06
Matches are distributed among these distances:
24 1 0.00
25 42 0.06
26 2 0.00
27 1 0.00
28 2 0.00
29 3 0.00
30 657 0.89
31 9 0.01
33 1 0.00
34 2 0.00
35 3 0.00
36 2 0.00
37 2 0.00
38 1 0.00
40 5 0.01
41 9 0.01
ACGTcount: A:0.48, C:0.19, G:0.13, T:0.19
Consensus pattern (30 bp):
AAGCAATGATCCTCAACCAGGATTAAAATA
Found at i:44971 original size:41 final size:41
Alignment explanation
Indices: 44914--44993 Score: 133
Period size: 41 Copynumber: 2.0 Consensus size: 41
44904 CAGGATTAAA
*
44914 ATAAAACAATGATCCTCAAACAGGATTAAAATAAAGCAATG
1 ATAAAACAATGATCCTCAAACAGGATTAAAACAAAGCAATG
* *
44955 ATAAAGCAATGATCCTCAACCAGGATTAAAACAAAGCAA
1 ATAAAACAATGATCCTCAAACAGGATTAAAACAAAGCAA
44994 CAATCCTAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.53, C:0.17, G:0.12, T:0.17
Consensus pattern (41 bp):
ATAAAACAATGATCCTCAAACAGGATTAAAACAAAGCAATG
Found at i:45000 original size:71 final size:71
Alignment explanation
Indices: 44884--45023 Score: 210
Period size: 71 Copynumber: 2.0 Consensus size: 71
44874 CAGGATTAAA
* ** *
44884 ATAAAGCAATGATCCTAAACCAGGATTAAAATAAAACAATGATCCTCAAA-CAGGATTAAAATAA
1 ATAAAGCAATGATCCTAAACCAGGATTAAAACAAAACAACAATCCT-AAACCAGGATTAAAACAA
44948 AGCAATG
65 AGCAATG
* *
44955 ATAAAGCAATGATCCTCAACCAGGATTAAAACAAAGCAACAATCCTAAACCAGGATTAAAACAAA
1 ATAAAGCAATGATCCTAAACCAGGATTAAAACAAAACAACAATCCTAAACCAGGATTAAAACAAA
45020 GCAA
66 GCAA
45024 CAATCCTAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
70 3 0.05
71 59 0.95
ACGTcount: A:0.52, C:0.19, G:0.12, T:0.17
Consensus pattern (71 bp):
ATAAAGCAATGATCCTAAACCAGGATTAAAACAAAACAACAATCCTAAACCAGGATTAAAACAAA
GCAATG
Found at i:45988 original size:36 final size:36
Alignment explanation
Indices: 45946--46146 Score: 258
Period size: 36 Copynumber: 5.6 Consensus size: 36
45936 ATCCTGGATC
* * *
45946 AATTAAAGAAAAGATCACCCTCGATCAACTGAAATA
1 AATTAAAGAAAAGATCGCCCTGGATCAATTGAAATA
* * *
45982 AGTTAAAGAAAAGATCGCCCTTGATCAATTGAACTA
1 AATTAAAGAAAAGATCGCCCTGGATCAATTGAAATA
* * * *
46018 AACTGAAGAAAAGATTGTCCTGGATCAATTGAAATA
1 AATTAAAGAAAAGATCGCCCTGGATCAATTGAAATA
*
46054 AATTAAAGAAAAGATCGCCCTGGATCAACTGAAATA
1 AATTAAAGAAAAGATCGCCCTGGATCAATTGAAATA
* * * *
46090 AACTGAAGAAAAGATTGTCCTGGATCAATTGAAATA
1 AATTAAAGAAAAGATCGCCCTGGATCAATTGAAATA
*
46126 AATTAAATAAAAGATCGCCCT
1 AATTAAAGAAAAGATCGCCCT
46147 AAAAAGATGC
Statistics
Matches: 138, Mismatches: 27, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 138 1.00
ACGTcount: A:0.46, C:0.15, G:0.16, T:0.23
Consensus pattern (36 bp):
AATTAAAGAAAAGATCGCCCTGGATCAATTGAAATA
Found at i:46051 original size:72 final size:72
Alignment explanation
Indices: 45968--46146 Score: 304
Period size: 72 Copynumber: 2.5 Consensus size: 72
45958 GATCACCCTC
* * * * *
45968 GATCAACTGAAATAAGTTAAAGAAAAGATCGCCCTTGATCAATTGAACTAAACTGAAGAAAAGAT
1 GATCAATTGAAATAAATTAAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAAGAT
46033 TGTCCTG
66 TGTCCTG
46040 GATCAATTGAAATAAATTAAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAAGAT
1 GATCAATTGAAATAAATTAAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAAGAT
46105 TGTCCTG
66 TGTCCTG
*
46112 GATCAATTGAAATAAATTAAATAAAAGATCGCCCT
1 GATCAATTGAAATAAATTAAAGAAAAGATCGCCCT
46147 AAAAAGATGC
Statistics
Matches: 101, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 101 1.00
ACGTcount: A:0.45, C:0.15, G:0.17, T:0.23
Consensus pattern (72 bp):
GATCAATTGAAATAAATTAAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAAGAT
TGTCCTG
Found at i:47624 original size:16 final size:17
Alignment explanation
Indices: 47599--47639 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
47589 TAGAAAACCA
47599 TTTTTG-AAAAATCATT
1 TTTTTGAAAAAATCATT
* *
47615 TTTTTTAAAAAATC-CT
1 TTTTTGAAAAAATCATT
47631 TTTTTGAAA
1 TTTTTGAAA
47640 GCAAGTGACT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.37, C:0.07, G:0.05, T:0.51
Consensus pattern (17 bp):
TTTTTGAAAAAATCATT
Found at i:47625 original size:17 final size:17
Alignment explanation
Indices: 47599--47635 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
47589 TAGAAAACCA
*
47599 TTTTTGAAAAATCATTT
1 TTTTTAAAAAATCATTT
*
47616 TTTTTAAAAAATCCTTT
1 TTTTTAAAAAATCATTT
47633 TTT
1 TTT
47636 GAAAGCAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.32, C:0.08, G:0.03, T:0.57
Consensus pattern (17 bp):
TTTTTAAAAAATCATTT
Found at i:55542 original size:21 final size:22
Alignment explanation
Indices: 55516--55558 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
55506 TTTGCCTCAT
55516 GCATTCATTCAT-CATACCATG
1 GCATTCATTCATGCATACCATG
* *
55537 GCATTCGTTCATGCATTCCATG
1 GCATTCATTCATGCATACCATG
55559 AAGCCTTAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.23, C:0.28, G:0.14, T:0.35
Consensus pattern (22 bp):
GCATTCATTCATGCATACCATG
Done.